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Green revolution for grains

In his lab, Thomas Ott aims to get cereal crops such as wheat and barley to grow Rhizobiaceae bacteria, as legume plants do. Photo: Jürgen Gocke

Some plants live in symbiosis with bacteria. In exchange for sugar, the microorganisms provide fertilizer. At the Excellence Cluster CIBSS – Centre for Integrative Biological Signalling Studies, cell biologist Professor Thomas Ott aims to also give grains the ability to enter into this symbiosis. Existing wheat, barley and other staple crops cannot form these partnerships. Once established, the principle should be applicable in all plant families. This international research project therefore has the potential to improve food supplies worldwide.

Thomas Ott – together with an international research consortium – is planning a revolution. A green revolution. The Freiburg cell biologist conducts research on nanodomains. These are the clusters of proteins that plant cells use to communicate with one another and to respond to external influences like nutrients or bacteria. “These signalling processes almost always involve nanodomains,” says Ott. In the CIBSS Excellence Cluster, he is focusing on a specific process, namely how legume plants attract the Rhizobiaceae bacteria. In this partnership, the microbes receive nutrients from the plants and deliver fertilizer in return. That is why researchers are seeking to couple cereal plants with Rhizobiaceae. Even in poor soils, the new type of grain could flourish without fertilizers.

A complicated relationship

Many open questions surround the symbiotic deal between bacteria and legumes. “Self-fertilizing cereals is a mammoth project,” emphasizes Ott. It is under the patronage of the Bill & Melinda Gates Foundation. Their ENSA program (Engineering Nitrogen Symbiosis for Africa) is led by the Sainsbury Laboratory and Cambridge University and provides support for about a dozen research teams around the world. First, they want to make barley accept Rhizobiaceae as partners. “Our CIBSS project is closely linked to ENSA,” Ott says. Both sides benefit: ENSA from the results produced in Freiburg, and Ott’s CIBSS project from ENSA resources such as services, data and materials. “This ambitious joint project gives us the chance to do unique experiments for which we would not normally have the framework.”

Biological signals and signalling pathways

Precise coordination is needed in order for trillions of cells to form, maintain and regenerate orderly tissues, organs and healthy organisms. To achieve this, complex communications processes take place between and within cells. Defects in these communications networks can lead to developmental disorders, immunodeficiency, cancer and other diseases. The CIBSS Cluster aims to achieve a comprehensive understanding of these communications processes – from the molecular level to the level of cells and organs. Furthermore, CIBSS research groups will investigate how these communications processes are connected to other important biological processes such as metabolism. Based on these new findings, the researchers will develop new possibilities to address challenges in areas as diverse as immunotherapy and the sustainable production of crops.

Plants are initially highly suspicious of soil bacteria, according to Ott, “Many bacteria can cause disease in plants.” This is why Rhizobiaceae identify themselves when they get near the roots of legume plants. “They say ‘I’m the right partner for you’,” explains Ott. The cell membrane contains receptors with which the plant ‘hears’ this greeting. If the greeting is accepted, the receptors join up with other proteins and form a nanodomain. “These are ordered clusters of proteins that are active in the same signalling pathway,” says Ott. His group has found that the scaffold proteins are needed to pull the receptors into the nanodomain. “The clustering doesn’t work without the scaffold proteins,” he says. Lone receptors are removed from the cell membrane and broken down. That means that without scaffold proteins there can be no symbiosis.

Night sky on the cell surface

Ott suspects that barley will need more than the legume entry receptors: “We will probably have to install a suitable nanodomain.” That means protein clusters of up to one micrometer. Nanodomains may contain two, three or more protein complexes and often have several tasks. They distinguish friend from foe, respond to nutrients in the environment, initiate cellular reactions and coordinate the cell’s behavior. A great deal of exchange takes place at nanodomains. They carry – at least transiently – further proteins, both inside and out. In this way, nanodomains receive different stimuli and signals, transmit messages through the cell membrane into the cell.

If Thomas Ott’s research project works out, crops will go fertilize themselves - with the prospect of 30 percent higher yields. Photo: photoschmidt/stock.adobe.com

“We can visualize nanodomains very well,” Ott says, presenting images taken with a microscope. They show structured surfaces with bright dots - “the night sky on the cell surface.” Each tiny star is a nanodomain containing proteins marked with a fluorescent tag. This is the type of domain through which the Rhizobiaceae make their pact with the peas. If the chemistry is right, the plant’s root cells switch to symbiosis mode. The root hairs fold up and surround the bacterium. At the same time, deeper in the tissue, nodules grow forming the bacteria’s future home. “During these processes, an incredible number of signalling events are occurring over a broad range of scales,” Ott explains. Later, the signalling processes also regulate symbiotic trade. The Rhizobiaceae fix gaseous nitrogen from the atmosphere and deliver this fertilizer to the legumes. In return, the plant feeds the bacteria with the sugar it produces via photosynthesis.

Filming live cells in real time

But what does barley need in order to partner up with the bacteria – to recognize them and respond positively? Which proteins are needed, and how many of each? Do they all have to come together in one nanodomain? Ott and his 14-person team are currently working on such questions. Starting in barley they will use individually marked proteins to assemble nanodomains with entry receptors. “We want to see the bright little dots on the barley cells under the microscope.” After that, the researchers will remove or mutate individual proteins and see what happens when they introduce Rhizobiaceae to such barley plants. Will the engineered nanodomains pass on the signals? Will barley cells break down the entry receptors if the scaffold proteins are missing? In which ways are barley and legumes alike, and how do they differ?

Protein complexes may be seen on the puzzle-piece-like cell of a leaf. These tiny dots are composed of molecular scaffold proteins and cell surface receptors; without them, there can be no symbiosis between plants and Rhizobiaceae. Source: Thomas Ott

Along with molecular biology, modern microscopy techniques are important tools. “With these techniques we can observe and film protein complexes in living cells in real time,” Ott says. It is possible to resolve how proteins find one another, stay together, and break up - even down to a billionth of a second. With this advanced microscopy, Ott can also tell whether friendly signals reach the cell nucleus: “If perception and transmission take place correctly, the nucleus discharges waves of calcium.” A reporter protein that lights up in the presence of calcium then starts to blink rhythmically.

30 percent higher yield

“Within the framework of CIBSS, we aim to functionally reconstruct the entry nanodomain,” Ott says. He even hopes to be able to transmit partnership signals to the barley and see the plant respond accordingly. “Self-fertilizing cereal crops are my dream,” says Ott, who studied biology in Göttingen and Manchester. His path led via Potsdam-Golm and Toulouse to Munich, where he worked as a postdoc, research group leader, and later as a professor of genetics. The University of Freiburg recruited him to the southwest in 2016 with a family-friendly offer. Ott praises the top research environment in Freiburg, then returns to the long-term goal of his career. Self-fertilizing cereal crops would not need fertilizers, nor more water than other crops but could produce a 30 percent higher yield. Once established, the principle should be applicable in all plant families. “Globally, this would have an enormous effect on food security and sustainable agriculture,” Ott explains. “At the very least, I would like to have made an important contribution to this.”

Jürgen Schickinger

CIBSS – Centre for Integrative Biological Signaling Studies

CIBSS is one of the two new Clusters of Excellence at the University of Freiburg. In CIBSS, more than 60 working groups will investigate biological signalling processes of immune cells and mitochondria, and in organ development and in plant roots. The researchers come from six faculties – for Biology, Mathematics and Physics, Medicine, Chemistry and Pharmacy, Engineering, and Law. The University Medical Center and the Max Planck Institute of Immunobiology and Epigenetics are also participating in CIBSS. The German Research Foundation (DFG) is funding the Cluster from the beginning of 2019 until the end of 2025.